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EP4276194A3 - Methods and processes for non-invasive assessment of genetic variations - Google Patents

Methods and processes for non-invasive assessment of genetic variations Download PDF

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Publication number
EP4276194A3
EP4276194A3 EP23193976.0A EP23193976A EP4276194A3 EP 4276194 A3 EP4276194 A3 EP 4276194A3 EP 23193976 A EP23193976 A EP 23193976A EP 4276194 A3 EP4276194 A3 EP 4276194A3
Authority
EP
European Patent Office
Prior art keywords
bases
less
reads
fragment length
nucleic acid
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP23193976.0A
Other languages
German (de)
French (fr)
Other versions
EP4276194A2 (en
Inventor
Cosmin Deciu
Sung K. Kim
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Sequenom Inc
Original Assignee
Sequenom Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US13/782,883 external-priority patent/US10504613B2/en
Priority claimed from US13/782,857 external-priority patent/US9920361B2/en
Application filed by Sequenom Inc filed Critical Sequenom Inc
Publication of EP4276194A2 publication Critical patent/EP4276194A2/en
Publication of EP4276194A3 publication Critical patent/EP4276194A3/en
Pending legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6879—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for sex determination
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention relates to a system comprising one or more processors and memory, which memory comprises instructions executable by the one or more processors, and which instructions executable by the one or more processors are configured to: (a) access nucleotide sequence reads mapped to a subset of genomic sections of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample from a pregnant subject, wherein the subset consists essentially of genomic sections to which an enriched amount of reads from fetal nucleic acid fragments are mapped, wherein the subset of genomic sections is selected according to a fragment length ratio XIY for each genomic section, wherein: X is the sum of reads that (i) map to the genomic section, and (ii) are from nucleic acid fragments that are shorter than a first selected fragment length, wherein the first selected fragment length is about 160 bases or less, about 150 bases or less, or about 140 bases or less; and Y is the sum of reads that (i) map to the genomic section, and (ii) are from nucleic acid fragments that are shorter than a second selected fragment length, wherein the second selected fragment length is about 1000 bases or less, about 600 bases or less, or about 200 bases or less; (b) determine the amount of sequence reads mapped to the subset of genomic sections; and (c) determine the presence or absence of a copy number variation according to the amount determined in (b).
EP23193976.0A 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations Pending EP4276194A3 (en)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US201261649841P 2012-05-21 2012-05-21
US201261740368P 2012-12-20 2012-12-20
US201261740377P 2012-12-20 2012-12-20
US13/782,883 US10504613B2 (en) 2012-12-20 2013-03-01 Methods and processes for non-invasive assessment of genetic variations
US13/782,857 US9920361B2 (en) 2012-05-21 2013-03-01 Methods and compositions for analyzing nucleic acid
EP13726373.7A EP2852680B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP19219319.1A EP3663409B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
PCT/US2013/041906 WO2013177086A1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP21201053.2A EP3978621B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations

Related Parent Applications (3)

Application Number Title Priority Date Filing Date
EP21201053.2A Division EP3978621B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP19219319.1A Division EP3663409B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP13726373.7A Division EP2852680B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations

Publications (2)

Publication Number Publication Date
EP4276194A2 EP4276194A2 (en) 2023-11-15
EP4276194A3 true EP4276194A3 (en) 2024-03-06

Family

ID=52105674

Family Applications (4)

Application Number Title Priority Date Filing Date
EP13726373.7A Active EP2852680B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP23193976.0A Pending EP4276194A3 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP19219319.1A Active EP3663409B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP21201053.2A Active EP3978621B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations

Family Applications Before (1)

Application Number Title Priority Date Filing Date
EP13726373.7A Active EP2852680B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations

Family Applications After (2)

Application Number Title Priority Date Filing Date
EP19219319.1A Active EP3663409B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations
EP21201053.2A Active EP3978621B1 (en) 2012-05-21 2013-05-20 Methods and processes for non-invasive assessment of genetic variations

Country Status (6)

Country Link
EP (4) EP2852680B1 (en)
CA (1) CA2874195C (en)
DK (2) DK2852680T3 (en)
ES (2) ES2902401T3 (en)
HK (1) HK1205203A1 (en)
WO (1) WO2013177086A1 (en)

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Also Published As

Publication number Publication date
EP2852680A1 (en) 2015-04-01
EP3663409A1 (en) 2020-06-10
CA2874195C (en) 2020-08-25
DK2852680T3 (en) 2020-03-16
CA2874195A1 (en) 2013-11-28
EP3663409B1 (en) 2021-10-06
WO2013177086A1 (en) 2013-11-28
ES2772029T3 (en) 2020-07-07
DK3663409T3 (en) 2021-12-13
HK1205203A1 (en) 2015-12-11
EP3978621B1 (en) 2023-08-30
ES2902401T3 (en) 2022-03-28
EP3978621A1 (en) 2022-04-06
EP4276194A2 (en) 2023-11-15
EP2852680B1 (en) 2019-12-25

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